Contacts of the helix formed by residues 469 - 486 (chain G) in PDB entry 5X8Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 469 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359G GLU* 3.4 37.5 + - + +
362G LEU* 4.3 4.0 - - + +
363G VAL* 5.3 0.7 - - + -
403G PHE* 3.5 28.7 - - + -
467G PRO 3.6 2.6 + - - +
468G PRO* 1.3 73.7 - - - +
470G GLY* 1.3 65.5 + - - +
471G LYS 3.4 2.7 - - - -
472G LEU* 3.5 7.6 + - - +
473G ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 470 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359G GLU* 4.3 11.6 + - - -
468G PRO* 3.7 1.4 - - - +
469G ALA* 1.3 77.0 - - - +
471G LYS* 1.3 61.8 + - - +
473G ALA* 3.4 4.8 + - - +
474G SER* 3.1 29.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 471 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399G SER* 5.0 6.7 + - - -
468G PRO 5.4 2.6 - - - +
469G ALA 3.4 0.6 - - - -
470G GLY* 1.3 76.5 - - - +
472G LEU* 1.3 83.7 + - + +
474G SER* 3.4 7.9 + - - -
475G LEU* 3.3 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 472 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G LEU* 3.7 16.2 - - + -
396G LEU* 4.5 7.4 - - + +
399G SER* 3.7 27.8 - - - +
400G ILE* 4.2 18.4 - - + -
403G PHE* 3.6 40.8 - - + -
468G PRO 4.9 6.2 + - - +
469G ALA 3.5 7.0 + - - +
470G GLY 3.4 0.2 - - - -
471G LYS* 1.3 102.6 - - + +
473G ALA* 1.3 66.3 + - - +
475G LEU* 3.2 10.8 + - + +
476G CYS* 3.1 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 473 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358G MET* 3.3 13.6 - - + +
359G GLU* 3.7 31.9 - - + +
362G LEU* 3.5 11.8 - - + +
469G ALA 3.1 15.4 + - - +
470G GLY* 3.8 4.9 - - - +
472G LEU* 1.3 80.3 - - - +
474G SER* 1.3 58.8 + - - +
476G CYS* 3.5 0.4 + - - -
477G SER* 2.9 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 474 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470G GLY 3.1 19.1 + - - -
471G LYS* 3.5 7.8 - - - -
472G LEU 3.2 0.2 - - - -
473G ALA* 1.3 79.1 - - - +
475G LEU* 1.3 59.0 + - - +
477G SER* 3.2 7.0 + - - -
478G GLN* 2.9 43.9 + - - +
2345H THR* 5.4 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396G LEU* 4.1 27.6 - - + -
471G LYS* 3.3 27.1 + - + +
472G LEU* 3.2 12.2 + - + +
474G SER* 1.3 78.6 - - - +
476G CYS* 1.3 57.6 + - - +
478G GLN* 3.4 21.8 + - + +
479G HIS* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 476 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G TRP* 6.2 0.4 - - - -
324G LEU* 4.6 12.1 - - + +
358G MET* 3.9 21.8 - - + -
362G LEU* 4.3 16.4 - - - -
396G LEU* 4.5 4.0 - - - -
400G ILE* 3.9 28.0 - - - -
472G LEU 3.1 18.4 + - - -
473G ALA 3.8 6.3 - - - +
475G LEU* 1.3 74.8 - - - +
477G SER* 1.4 56.5 + - - +
479G HIS* 3.3 8.5 + - - +
480G VAL* 3.0 31.9 + - - +
9000G 82R 4.4 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 477 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358G MET* 3.3 26.3 - - - +
473G ALA 2.9 19.6 + - - -
474G SER 3.6 4.7 - - - -
476G CYS* 1.4 71.5 - - - +
478G GLN* 1.3 60.7 + - - +
480G VAL* 3.3 5.7 + - - +
481G GLU* 3.0 23.2 + - - +
2345H THR 3.6 21.3 + - - -
2346H ASN* 3.1 24.0 + - - +
2349H LEU* 3.9 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 478 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G SER* 2.9 29.0 + - - +
475G LEU* 3.6 21.3 - - + +
477G SER* 1.3 75.0 - - - +
479G HIS* 1.3 59.1 + - + +
481G GLU* 3.2 7.2 + - - +
482G ARG* 2.8 29.7 + - - +
2346H ASN* 3.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 479 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G TRP* 3.5 32.7 - + + -
393G CYS* 3.6 24.0 - - - -
396G LEU* 3.5 25.2 - - + +
475G LEU* 3.0 26.3 + - + +
476G CYS* 3.3 8.9 + - - +
478G GLN* 1.3 77.1 - - + +
480G VAL* 1.3 64.5 + - + +
482G ARG* 3.1 38.1 + - - +
483G LEU* 3.1 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 480 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G TRP* 6.3 0.2 - - + -
321G ALA* 4.6 16.6 - - + +
324G LEU* 3.9 34.1 - - + -
325G THR* 4.3 7.9 - - - +
358G MET* 4.1 10.5 - - + -
476G CYS 3.0 17.0 + - - +
477G SER* 3.5 10.1 - - - +
478G GLN 3.2 0.2 - - - -
479G HIS* 1.3 76.3 - - - +
481G GLU* 1.3 62.2 + - - +
483G LEU* 3.6 4.0 + - - +
484G GLN* 3.3 35.3 + - + +
2348H GLY 5.3 1.8 - - - -
2349H LEU* 4.7 5.6 - - + -
2352H ILE* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 481 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477G SER 3.0 11.1 + - - +
478G GLN* 3.6 7.1 - - - +
480G VAL* 1.3 76.2 - - - +
482G ARG* 1.3 66.1 + - - +
484G GLN* 3.0 9.6 + - + +
485G ILE* 3.0 42.9 + - + +
2346H ASN* 3.5 31.8 + - - +
2347H MET* 3.3 15.2 + - - +
2348H GLY* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 482 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G MET* 6.2 0.6 - - - +
317G TRP* 3.5 26.1 - - - +
478G GLN 2.8 17.6 + - - +
479G HIS* 3.1 37.5 + - - +
481G GLU* 1.3 72.8 - - - +
483G LEU* 1.3 89.3 + - - +
485G ILE* 3.3 14.4 + - - -
486G PHE* 3.3 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 483 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G TRP* 5.1 9.2 - - + +
317G TRP* 3.5 48.2 - - + +
318G GLU* 3.7 13.5 - - + +
321G ALA* 3.7 16.2 - - + -
479G HIS 3.1 16.7 + - - +
480G VAL 3.9 5.4 - - - +
482G ARG* 1.3 113.0 - - - +
484G GLN* 1.3 62.8 - - + +
486G PHE* 4.1 2.1 - - - -
487G GLN* 3.6 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 484 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G THR* 5.3 0.3 + - - -
480G VAL* 3.3 16.2 + - + +
481G GLU* 3.0 9.5 + - + +
483G LEU* 1.3 79.5 - - - +
485G ILE* 1.3 64.5 + - + +
486G PHE 3.4 0.3 + - - -
487G GLN* 3.1 31.5 - - - +
2348H GLY* 3.2 42.6 + - - +
2351H ALA* 4.4 10.3 - - - +
2352H ILE* 3.6 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 485 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481G GLU* 3.0 44.5 + - + +
482G ARG* 3.3 8.5 + - - +
484G GLN* 1.3 79.3 - - + +
486G PHE* 1.3 85.8 + - + +
487G GLN* 3.5 2.7 + - - +
488G HIS* 5.0 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 486 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482G ARG* 3.3 43.4 + - + +
483G LEU* 4.1 4.3 - - - +
484G GLN 3.2 0.6 - - - -
485G ILE* 1.3 100.9 - - + +
487G GLN* 1.3 61.2 + - - +
488G HIS* 3.1 4.3 + - - -
489G LEU* 3.2 30.8 + - + +
490G HIS* 3.0 32.1 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il